Crap!... Quick test and looks worst then what you describe actually, as in "new last second bug in Premiere CS4"... let me see what I can do this week (if I can actually lie to Premiere so it returns the proper values). That said, do you see this with Quicktime movies, AVI or what (with fields, no fields) - so I can test all cases...

I reported the following bug to Premiere 4.0.0
"If you trim the begining of a clip in your edit timeline, then Premiere CS4.0.0 returns the wrong current time value to plug-in. There are workarounds, for Twixtor since often you need anyway to create a new sequence if you want to make the sequence longer, you simply need for now to make the in-point edit inside the nested sequence. Hopefully it will be fixed in 4.0.1 dot release"